A senior Al-Qaeda operative and envoy in Syria of its leader, Ayman al-Zawahiri, has been killed by a suicide bomber in factional fighting near Aleppo.

Abu Khalid al-Suri worked for Osama bin Laden from at least the 1990s, according to Western intelligence agencies, and had been appointed by Zawahiri as his personal envoy to mediate disputes among followers in the Syrian rebel movement.

The group Suri helped found, Ahrar al-Sham, is now one of the most powerful factions in Syria but had fallen out with the Islamic State of Iraq and al-Sham (ISIS), the most violent jihadist group that was formally disavowed by Al-Qaeda earlier this month.

The two bombers managed to get inside the Ahrar al-Sham base in Aleppo and blow themselves up on Sunday morning.

The attack was immediately blamed by Ahrar al-Sham on ISIS, setting off furious arguments by supporters of each on the social media used avidly by many jihadist groups in Syria.

Another Suri supporter claimed he had said earlier this month that the group had threatened to send suicide attackers after him.

Suri’s personal history was as mysterious as much of the network’s history before and after the 9/11 attacks in 2001.

A Syrian, as indicated by his nom de guerre, his real name was said to be Mohammed al-Bahaiah and he was used to ferry Osama bin Laden’s money to his operatives around the world.

He was implicated in attacks as far afield in Yemen and Spain including the 2004 attack on metro lines in Madrid that killed 191.

At some point he disappeared from view and turned up in prison in Syria - analysts believe as a result of the US “rendition” programme under which suspected militants were turned over to Middle Eastern governments with lower legal thresholds for jailing, and torturing, their foes.

Some ISIS commanders denied the group was responsible. Another theory for al-Suri's death was that he might have been killed following splits in Ahrar al-Sham's own leadership - with some analysts pointing out that with him gone it would be easier to obtain supports from American allies.

He is thought then to have been released along with other Islamist militants under an amnesty ordered by President Bashar al-Assad early in the uprising against him. Another beneficiary of the “amnesty” - now seen by regime opponents as a deliberate attempt to colour a secular uprising with a militant brush - was Hassan Aboud, with whom he founded Ahrar al-Sham.

Last year, the formal wing of al-Qaeda in Syria, Jabhat al-Nusra, split in two, with Jabhat swearing allegiance to Zawahiri and the remainder declaring itself part of Islamic State of Iraq and al-Sham, under the Iraqi al-Qaeda leader Abu Bakr al-Baghdadi. ISIS has gone on to win a reputation for brutality and in particular the beheadings of captives.

Zawahiri ordered Suri to mediate, but after his failure declared that ISIS was no longer part of Al-Qaeda. If Sunday’s attack was revenge, it indicate a new phase of the battle for the soul of international jihad with the edicts of “Al-Qaeda Centre” more open to direct challenge by so-called “affiliates”.

“Seeing as Zawahiri had appointed him as his personal intermediary his killing will be felt further afield than just Syria,” Charles Lister, an analyst who monitors jihadi groups at the Brookings Institution in Doha said.

The whole northern front of the rebel movement in Syria has been riven by fighting between ISIS and other groups, both secular and Islamist like Ahrar al-Sham, determined to drive it out, partly at the encouragement of Saudi Arabia and particularly the United States, which is reluctant to arm the rebels because of the jihadist presence.

The fight against ISIS has been only partially successful, and it retains its strongholds in Raqqa province and towns north-east of Aleppo. It is also fighting back against the groups that have taken it on and against civilians in areas they hold.

It was blamed by local activists for another bomb on Sunday morning, this time in Atmeh, a border village with Turkey from which it was forced to withdraw last month. The bomb hit a hospital funded by a Syrian exile businessman for refugees, killing and injuring scores of people including doctors, nurses and patients, according to activists in the town.

The number of dead was unclear, with many survivors being taken to Turkey for treatment, but one activist, speaking by Skype, said 13 people were killed and 63 injured, including a five-month baby gravely wounded by shrapnel.